A once-in-500 year storm has slammed Northland, flooding shops and forcing residents to evacuate homes.

Fire crews rushed out to 212 emergency call outs as the storm dumped 220mm on Whangarei.

The heavy falls caused slips and landslides that closed roads and limited water supplies.

Whangarei residents are this morning being asked to conserve water after the city's water treatment plants were "struggling to cope with the intense rainfall", the Whangarei District Council said.

Residents in Onerahi and Whangarei Heads were advised not to drink or use tap water except in emergencies after a burst water main on Riverside Dr had affected water supply.

And the drama isn't over yet.

A MetService severe thunderstorm watch remains in force for Northland until 10.30am, meaning waking residents could be in for further flooding and damage.

Meteorologist Alwyn Bakker said the intense storm had been created by the unusual interaction between two low pressure zones in a manner that caused a direct hit on Northland.

"We've done some calculations over here in MetService," Bakker said of the storm.

"And 220mm for Whangarei has what we call a greater than 500 year return period."

"What that means is we see this kind of thing once in every 500 years."

Bakker said MetService's continued thunderstorm watch meant rainfalls between 40-60mm an hour could still fall this morning.

By the afternoon, however, the storm should break and turn to periods of showers later in the day before petering off tomorrow.

Murray Soljack, from Northland Civil Defence and Emergency Management, said fire crews carried the brunt of the emergency response overnight, rescuing people trapped in cars in floodwaters and helping evacuate people from homes.

He estimated about 30 people had evacuated homes across Northland with 12 in Whangarei requiring assistance from fire crews.

Some relocated to the two Civil Defence welfare centres set up in the Kamo Scout Hall and Onerahi Community Hall.

Luckily no one appeared to be injured, Soljak said.

Today would be all about making an assessment of the damage, putting priorities around that and seeing how long it will take to restore services, he said.

Between the flooding, damaged roads and slips there was a lot to be done across the region this morning, he said.

He asked residents to stay off the roads today.

Civil Defence emergency management officer Claire Nyberg, who was manning the Civil Defence Centre at the Onerahi Community Hall, said she had been set up since 8pm yesterday.

Nyberg said only one person had been evacuated from their home and brought to the centre.

Nyberg, who had worked with Civil Defence for 12 years, said last night's rainfall was comparable to when tropical cyclone Wilma hit New Zealand and some Pacific islands in 2011.

The wild storms yesterday evening left a group of 12 stranded in waist-high swirling water at a flooded Whangarei petrol station.

The BP petrol station in Riverside Drive, Parahaki, Whangarei, was flooded after water started seeping under the door at 7.30pm.

A BP staff member there told the Herald a group of customers were stuck at the station.

"In the deepest spot it's probably waist deep. The whole place is pretty much under water. There's waves coming in the shop when people drive past and what not," he said.

The 25-year-old BP staffer said eight cars were stuck in the car park with water lapping at the sides about 9.30pm last night.

"Yeah pretty much [standing in water]. We've got a couple of customers here who are all trapped. So everyone here is pretty much trapped here at the moment," he said.

The staffer said the group of staff and customers stranded were calm.

Everyone's pretty much chilling out talking and drinking coffee and eating pies," he said.

Floodwaters also hit The Real Cornish Pasty Company in Onerahi, south of Whangarei.

"It's at least half way up my legs in the bakery at the moment," owner Derek O'Brien told the Herald.

"Everything in there is just floating around in the water."

O'Brien said the bakery was next to his home but it was now raining so heavily he couldn't get outside to check on his business again.

He said the floodwaters had come down the street, overwhelming the drains that council had cleared yesterday, and flowed under the doors of his business.

"It's like a tsunami coming down the hill".

He said he'd now be in cleanup mode this morning, rather than getting up early to bake about 200 pies and pastries.

Northland region hammered thunderstorms, lightning strikes, huge tornado

Severe thunderstorms hit the Northland region all day yesterday, but Whangarei was struck particularly hard.

At 7.30pm emergency services received multiple reports of people trapped in their cars due to flooding on State Highway 1 near Puketona in the Far North.

Today's wild weather: People trapped in cars, flooded homes abandoned in Far North, SH1 closed

Emergency services responded to more than 200 calls after flooded homes, people trapped in cars, a huge tornado and closed highways impacted the province.

Residents in the area were choosing to abandon their homes due to flooding.

"There has been heavy rain around the Whangarei area with multiple flooding events across the city," a Fire and Emergency spokesperson said.

"We recommend people stay safe in their homes and contact the local civil defence."

A resident in Cobble Lane, just off Rawhiti St in the Whangarei suburb of Morningside, said she could see people being evacuated from their homes near the hall.

It looked like they were wading through ankle deep water before climbing onto a big truck of some sort.

Police and Fire and Emergency both confirmed they were attending an job on Rawhiti St as of 8.30pm.

Murray Soljak, of Northland's Civil Defence Emergency Management, said it was not a state of emergency but he expected it to be a very busy night.

MetService forecaster Gerard Bellam said Whangārei had received the biggest thunderstorm of the day just before 7pm.

"Unfortunately tomorrow we've got periods of rain. Some possibly heavy falls, and there are some thunderstorms again also possible north of Whangārei," Bellam said.

"In the meantime we've nearly had about 50mm in the last hour in Whangārei airport just before 7pm. That's another thunderstorm."

Rain flooded parts of State Highway 1, closed roads between Okaihau and Kaitaia and at Moerewa near Bay of Islands.

Niwa reported 500-plus lightning strikes in Northland yesterday, and 125mm of rain in the Far North.

Elsewhere, a video of a huge tornado out at sea was filmed near Tupou Bay in the Far North after midday.

Bellam said the weather in Northland was forecast to be bad again today.